Certainly! The differences between a fuel pump with two valves and one with three valves are generally related to the vehicle's fuel system configuration and its specific fuel requirements. Here’s a detailed breakdown:

### Two-Valve Fuel Pump:
1. **Supply Line**: One valve will typically be for the fuel supply line, which sends fuel from the tank to the engine.
2. **Return Line**: The other valve may be for the return line, which recirculates unused fuel back to the tank. However, in some modern systems, especially those designed as "returnless" systems, the fuel return is managed differently and might not be present at the pump.

### Three-Valve Fuel Pump:
1. **Supply Line**: One valve is for the fuel supply line.
2. **Return Line**: The second valve handles the fuel return line.
3. **Evaporation (EVAP) or Fuel Vapor Line**: The third valve can be for the EVAP system or a fuel vapor line, which helps manage the fuel vapor emissions by sending them either back to the tank or to a charcoal canister for filtering.

### Why Both Types May Appear in Parts Stores:
- **Design Variations**: Different manufacturers might have variations in the fuel pump designs. Your vehicle might have been produced with slightly different configurations depending on the market, production date, or specific model options.
- **Emission Systems**: Vehicles with more complex emission control systems often have additional lines for managing fuel vapors, contributing to environmental compliance which explains the extra valve in some fuel pump designs.

### Which One is Correct for Your Vehicle?
To determine the exact fuel pump you need, consider the following steps:
1. **Check the VIN**: Using your vehicle's VIN (Vehicle Identification Number), you can accurately look up the correct part. Parts store databases often have VIN-specific parts listings that ensure you get the right component.
2. **Compare with the Original**: Compare the new fuel pump’s configuration closely with your original pump. Ensure that all the connections (valves) match in terms of position and function.
3. **Consult the Manual**: If you have access to a repair or service manual for your 2006 Chevrolet 3500, it should specify the correct fuel pump type.
4. **Consider Return or Returnless Systems**: Understand whether your vehicle uses a return or returnless fuel system. Returnless systems typically have fewer connections directly at the pump.

### Adapting a Three-Valve Pump to a Two-Valve System:
While it might be technically possible to use a three-valve pump in a two-valve system by capping or blocking the extra valve, this is not recommended unless you are certain of the implications for your vehicle's performance and safety. Always aim for an exact match to avoid potential issues.

If you need further guidance, please provide more context or specific parts numbers, and I'd be happy to help you further!